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Author Message
Kenward Vaughan
Posted on Friday, November 26, 2004 - 5:33 pm:   

Hello,

I've been playing with WebMO for about a day now, trying to get it to properly submit jobs to Gamess (this month's version :). Nothing has worked quite right yet, so I was hoping for some help.

I set up gamess to work through rungms, as it comes in the distribution. If I use the defaults in WebMO (ddikick.x and gamess.XX.x), the run fails since none of the variables are properly set up (which is normally done within rungms).

If I substitute "rungms" in for gamess.XX.x, the run sometimes completes properly from within gamess, despite ddikick dying afterwards. In these cases the environmental stuff is set twice, which I don't understand. For this method to work, I additionally had to modify rungms so the directory part of the input file information gets stripped off, since it expects the input file to be in the current directory at the time of execution.

A single point E. calc. survived this setup with rungms, but a geom. optimization did not (it dies during execution). Yet the same geom. opt. did fine when run without WebMO, using the file generated by WebMO and run through the same modified rungms executable.


Other variations (esp. leaving off ddikick.x totally) die as well.

How do people set this up?? What else can I provide information-wise? Many thanks for any help!

Kenward Vaughan
Department of Chemistry
Bakersfield College
http://www2.bc.cc.ca.us/kvaughan/

Following is my current gamess directory structure and the WebMO configuration list:

echo ----- GAMESS execution script -----
...
if ($JOBNAME:r.inp == $JOBNAME) set JOBNAME=$JOBNAME:r # strip off possible .

set JOB=`basename $JOBNAME`

if (-e $JOBNAME.inp) then
set echo
cp $JOBNAME.inp $SCR/$JOB.F05
unset echo
else
if (-e tests/$JOB.inp) then
set echo
cp tests/$JOB.inp $SCR/$JOB.F05
unset echo
else
echo "Input file $JOB.inp does not exist. Please fix and resubmit."
exit 4
endif
endif

# file assignments.
...
set echo
setenv ERICFMT /usr/local/bin/gamess/ericfmt.dat
setenv EXTBAS /dev/null
setenv IRCDATA /home/daddy/Chemistry/gamess/scr/$JOB.irc
setenv INPUT $SCR/$JOB.F05
setenv PUNCH /home/daddy/Chemistry/gamess/scr/$JOB.dat
setenv AOINTS $SCR/$JOB.F08
... (other variables follow) ...


--------WebMO stuff--------

backgroundGraphic="background_dna.gif"
catPath="/bin/cat"
cgiBase="/home/daddy/public_html/cgi-bin/webmo"
cpPath="/bin/cp"
externalBatchQueue=""
host="hpotter.vaughan.home"
htmlBase="/home/daddy/public_html/webmo"
killPath="/bin/kill"
license="0411-2405-4207"
mkdirPath="/bin/mkdir"
mvPath="/bin/mv"
owner="Computational Chemistry on the WWW"
perlPath="/usr/bin/perl"
psOptions="-ef"
psPath="/bin/ps"
psRegExp="(\$pid, \$ppid, \$cpu_time) = /.{8}(.{6})(.{6}).{3}.{6}.{5}(.{111}).*/"
rcpPath="/usr/bin/rcp"
rmPath="/bin/rm"
rshPath="/usr/bin/rsh"
scpOptions="-o Protocol=1"
scpPath="/usr/bin/scp"
sendmailOptions="-t"
sendmailPath="/usr/sbin/sendmail"
servers="hpotter.vaughan.home,0"
sshOptions="-o Protocol=1"
sshPath="/usr/bin/ssh"
systemScratch="/tmp"
tableBackgroundColor="#99cccc"
tarOptions="cf"
tarPath="/bin/tar"
unamePath="/bin/uname"
url_cgiBase="/users/daddy/cgi-bin/webmo"
url_htmlBase="/users/daddy/webmo"
userBase="/home/daddy/webmo"
version="4.1.003"
webserver="autodetect"
whereisPath="/usr/bin/whereis"
schmidt
Posted on Monday, November 29, 2004 - 10:24 am:   

A new environmental variable was added to the 22 NOV 2004 release of GAMESS. Add the line,

$ENV{'ERICFMT'} = "$gamessGMSPATH/ericfmt.dat";

to run_gamess.cgi. This change will be incorperated into WebMO 5. Thanks to Kenward Vaughan for the fix!

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